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NullModelNullModel
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adding files for v302 update
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+408
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lines changed

‎src/hg/mouseStuff/lavToPsl/tests/expected/newStyleLastz.bed‎

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##aligner=lastz.v1.03.46 M=50 T=2 O=400 E=30 Q=hg19.susScr3.chrM.Q.txt --output=hg19.susScr3.chrM.lav
2+
##matrix=lastz.v1.03.46 16 79,-84,-55,-128,-84,100,-174,-55,-55,-174,100,-84,-128,-55,-84,79
3+
##gapPenalties=lastz.v1.03.46 O=400 E=30
4+
##blastzParms=O=400,E=30,K=3000,L=3000,M=50
5+
hg19_chrM 575 16024 susScr3_chrM 496 + 575 16024 0 97 55,138,101,61,29,77,79,128,35,27,75,20,106,27,51,62,21,14,15,22,26,48,123,135,54,33,61,20,5,83,62,10,37,39,292,88,17,278,6,3,24,1065,123,31,35,26,15,30,953,18,15,34,21,20,68,9,71,86,36,17,1531,84,14,38,687,10,19,28,116,14,7,1513,402,13,37,836,14,1004,29,14,10,587,6,1178,245,8,264,77,692,18,427,17,31,13,16,36,15, 0,56,194,297,358,389,467,547,675,711,738,813,834,948,975,1027,1090,1113,1127,1142,1164,1190,1238,1361,1498,1554,1587,1649,1669,1675,1759,1821,1833,1871,1910,2202,2291,2308,2586,2596,2599,2623,3689,3812,3843,3878,3916,3931,3961,4914,4937,4953,4987,5009,5030,5098,5107,5178,5264,5301,5329,6860,6944,6959,6997,7689,7715,7735,7765,7884,7908,7915,9428,9830,9843,9880,10718,10732,11737,11766,11785,11795,12382,12391,13577,13822,13831,14095,14172,14864,14885,15313,15331,15362,15379,15397,15434,

‎src/hg/mouseStuff/lavToPsl/tests/expected/newStyleLastz.psl‎

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##aligner=lastz.v1.03.46 M=50 T=2 O=400 E=30 Q=hg19.susScr3.chrM.Q.txt --output=hg19.susScr3.chrM.lav
2+
##matrix=lastz.v1.03.46 16 79,-84,-55,-128,-84,100,-174,-55,-55,-174,100,-84,-128,-55,-84,79
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##gapPenalties=lastz.v1.03.46 O=400 E=30
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##blastzParms=O=400,E=30,K=3000,L=3000,M=50
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11494 3816 0 0 49 131 47 139 + susScr3_chrM 16613 1172 16613 hg19_chrM 16571 575 16024 97 55,138,101,61,29,77,79,128,35,27,75,20,106,27,51,62,21,14,15,22,26,48,123,135,54,33,61,20,5,83,62,10,37,39,292,88,17,278,6,3,24,1065,123,31,35,26,15,30,953,18,15,34,21,20,68,9,71,86,36,17,1531,84,14,38,687,10,19,28,116,14,7,1513,402,13,37,836,14,1004,29,14,10,587,6,1178,245,8,264,77,692,18,427,17,31,13,16,36,15, 1172,1227,1367,1468,1530,1559,1636,1715,1847,1882,1910,1991,2011,2117,2153,2204,2266,2287,2302,2320,2344,2371,2421,2545,2680,2734,2768,2829,2851,2856,2939,3002,3012,3049,3089,3385,3473,3491,3770,3776,3785,3812,4877,5001,5033,5069,5095,5113,5152,6110,6128,6143,6178,6199,6219,6288,6298,6370,6457,6493,6510,8047,8135,8149,8188,8875,8885,8904,8932,9048,9062,9082,10596,10999,11013,11053,11889,11905,12909,12940,12954,12967,13557,13563,14741,14987,14995,15262,15341,16036,16054,16481,16498,16533,16546,16562,16598, 575,631,769,872,933,964,1042,1122,1250,1286,1313,1388,1409,1523,1550,1602,1665,1688,1702,1717,1739,1765,1813,1936,2073,2129,2162,2224,2244,2250,2334,2396,2408,2446,2485,2777,2866,2883,3161,3171,3174,3198,4264,4387,4418,4453,4491,4506,4536,5489,5512,5528,5562,5584,5605,5673,5682,5753,5839,5876,5904,7435,7519,7534,7572,8264,8290,8310,8340,8459,8483,8490,10003,10405,10418,10455,11293,11307,12312,12341,12360,12370,12957,12966,14152,14397,14406,14670,14747,15439,15460,15888,15906,15937,15954,15972,16009,

‎src/hg/mouseStuff/lavToPsl/tests/expected/oldStyleBlastz.bed‎

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##aligner=blastz.v7 M=50 T=2 O=400 E=30 Q=hg19.susScr3.blastz.q
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##matrix=blastz.v7 16 79,-84,-55,-128,-84,100,-174,-55,-55,-174,100,-84,-128,-55,-84,79
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##gapPenalties=blastz.v7 O=400 E=30
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##blastzParms=O=400,E=30,K=3000,L=3000,M=50
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hg19_chrM 575 16022 susScr3_chrM 496 + 575 16022 0 97 55,138,101,61,29,77,79,128,35,27,75,20,106,27,51,62,21,14,15,22,26,48,123,135,54,33,61,20,5,83,62,10,37,39,292,88,17,278,6,3,24,1065,123,31,35,26,15,30,953,18,15,34,21,20,68,9,71,86,36,17,1531,84,14,38,687,10,19,28,116,14,7,1513,402,13,37,836,14,1004,29,14,10,587,6,1178,245,8,264,77,692,18,427,17,31,13,16,36,13, 0,56,194,297,358,389,467,547,675,711,738,813,834,948,975,1027,1090,1113,1127,1142,1164,1190,1238,1361,1498,1554,1587,1649,1669,1675,1759,1821,1833,1871,1910,2202,2291,2308,2586,2596,2599,2623,3689,3812,3843,3878,3916,3931,3961,4914,4937,4953,4987,5009,5030,5098,5107,5178,5264,5301,5329,6860,6944,6959,6997,7689,7715,7735,7765,7884,7908,7915,9428,9830,9843,9880,10718,10732,11737,11766,11785,11795,12382,12391,13577,13822,13831,14095,14172,14864,14885,15313,15331,15362,15379,15397,15434,

‎src/hg/mouseStuff/lavToPsl/tests/expected/oldStyleBlastz.psl‎

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##aligner=blastz.v7 M=50 T=2 O=400 E=30 Q=hg19.susScr3.blastz.q
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##matrix=blastz.v7 16 79,-84,-55,-128,-84,100,-174,-55,-55,-174,100,-84,-128,-55,-84,79
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##gapPenalties=blastz.v7 O=400 E=30
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##blastzParms=O=400,E=30,K=3000,L=3000,M=50
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11492 3816 0 0 49 131 47 139 + susScr3_chrM 16613 1172 16611 hg19_chrM 16571 575 16022 97 55,138,101,61,29,77,79,128,35,27,75,20,106,27,51,62,21,14,15,22,26,48,123,135,54,33,61,20,5,83,62,10,37,39,292,88,17,278,6,3,24,1065,123,31,35,26,15,30,953,18,15,34,21,20,68,9,71,86,36,17,1531,84,14,38,687,10,19,28,116,14,7,1513,402,13,37,836,14,1004,29,14,10,587,6,1178,245,8,264,77,692,18,427,17,31,13,16,36,13, 1172,1227,1367,1468,1530,1559,1636,1715,1847,1882,1910,1991,2011,2117,2153,2204,2266,2287,2302,2320,2344,2371,2421,2545,2680,2734,2768,2829,2851,2856,2939,3002,3012,3049,3089,3385,3473,3491,3770,3776,3785,3812,4877,5001,5033,5069,5095,5113,5152,6110,6128,6143,6178,6199,6219,6288,6298,6370,6457,6493,6510,8047,8135,8149,8188,8875,8885,8904,8932,9048,9062,9082,10596,10999,11013,11053,11889,11905,12909,12940,12954,12967,13557,13563,14741,14987,14995,15262,15341,16036,16054,16481,16498,16533,16546,16562,16598, 575,631,769,872,933,964,1042,1122,1250,1286,1313,1388,1409,1523,1550,1602,1665,1688,1702,1717,1739,1765,1813,1936,2073,2129,2162,2224,2244,2250,2334,2396,2408,2446,2485,2777,2866,2883,3161,3171,3174,3198,4264,4387,4418,4453,4491,4506,4536,5489,5512,5528,5562,5584,5605,5673,5682,5753,5839,5876,5904,7435,7519,7534,7572,8264,8290,8310,8340,8459,8483,8490,10003,10405,10418,10455,11293,11307,12312,12341,12360,12370,12957,12966,14152,14397,14406,14670,14747,15439,15460,15888,15906,15937,15954,15972,16009,

‎src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.bed.gz‎

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‎src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.psl.gz‎

263 KB
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‎src/hg/mouseStuff/lavToPsl/tests/input/hg19.chrom.sizes.gz‎

747 Bytes
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‎src/hg/mouseStuff/lavToPsl/tests/input/mm10.chrom.sizes.gz‎

529 Bytes
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‎src/hg/mouseStuff/lavToPsl/tests/input/newStyleLastz.lav‎

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#:lav
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d {
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"lastz.v1.03.46 hg19.chrM.fa susScr3.chrM.fa M=50 T=2 O=400 E=30 Q=hg19.susScr3.chrM.Q.txt --output=hg19.susScr3.chrM.lav
4+
A C G T
5+
79 -84 -55 -128
6+
-84 100 -174 -55
7+
-55 -174 100 -84
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-128 -55 -84 79
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O = 400, E = 30, K = 3000, L = 3000, M = 50"
10+
}
11+
#:lav
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s {
13+
"hg19.chrM.fa" 1 16571 0 1
14+
"susScr3.chrM.fa" 1 16613 0 1
15+
}
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h {
17+
">hg19_chrM"
18+
">susScr3_chrM"
19+
}
20+
a {
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s 660086
22+
b 576 1173
23+
e 16024 16613
24+
l 576 1173 630 1227 78
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32+
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33+
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34+
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35+
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36+
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}
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x {
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n 0
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}
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m {
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n 0
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}
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#:eof

‎src/hg/mouseStuff/lavToPsl/tests/input/oldStyleBlastz.lav‎

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#:lav
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d {
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"blastz.v7 hg19.chrM.fa susScr3.chrM.fa M=50 T=2 O=400 E=30 Q=hg19.susScr3.blastz.q
4+
A C G T
5+
79 -84 -55 -128
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-84 100 -174 -55
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-55 -174 100 -84
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-128 -55 -84 79
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O = 400, E = 30, K = 3000, L = 3000, M = 50"
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}
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#:lav
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s {
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"hg19.chrM.fa" 1 16571 0 1
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"susScr3.chrM.fa" 1 16613 0 1
15+
}
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h {
17+
">hg19_chrM"
18+
">susScr3_chrM"
19+
}
20+
a {
21+
s 659907
22+
b 576 1173
23+
e 16022 16611
24+
l 576 1173 630 1227 78
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33+
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35+
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}
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x {
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n 0
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}
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m {
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n 0
127+
}
128+
#:eof

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